The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computer assertion could be determined for this classification!


Variant: NM_000162.5(GCK):c.572G>A (p.Arg191Gln)

CA10604473

283358 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 572070cd-f397-46ce-86c0-08a594ad4b36
Approved on: 2024-04-19
Published on: 2024-04-19

HGVS expressions

NM_000162.5:c.572G>A
NM_000162.5(GCK):c.572G>A (p.Arg191Gln)
NC_000007.14:g.44149976C>T
CM000669.2:g.44149976C>T
NC_000007.13:g.44189575C>T
CM000669.1:g.44189575C>T
NC_000007.12:g.44156100C>T
NG_008847.1:g.44448G>A
NG_008847.2:g.53195G>A
ENST00000395796.8:c.*570G>A
ENST00000616242.5:c.572G>A
ENST00000682635.1:n.1058G>A
ENST00000345378.7:c.575G>A
ENST00000403799.8:c.572G>A
ENST00000671824.1:c.572G>A
ENST00000673284.1:c.572G>A
ENST00000345378.6:c.575G>A
ENST00000395796.7:c.569G>A
ENST00000403799.7:c.572G>A
ENST00000437084.1:c.521G>A
ENST00000616242.4:c.569G>A
NM_000162.3:c.572G>A
NM_033507.1:c.575G>A
NM_033508.1:c.569G>A
NM_000162.4:c.572G>A
NM_001354800.1:c.572G>A
NM_033507.2:c.575G>A
NM_033508.2:c.569G>A
NM_033507.3:c.575G>A
NM_033508.3:c.569G>A

Pathogenic

Met criteria codes 7
PM2_Supporting PS4 PP3 PP2 PP4_Moderate PM5_Supporting PP1_Strong
Not Met criteria codes 1
PM3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Monogenic Diabetes Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for GCK Version 1.3.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.605T>G variant in the glucokinase gene, GCK, causes an amino acid change of methionine to arginine at codon 202 (p.(Met202Arg)) of NM_000162.5. GCK is defined by the ClinGen MDEP as a gene that has a low rate of benign missense variation and has pathogenic missense variants as a common mechanism of disease (PP2). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.873, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant was identified in 39 unrelated individuals with hyperglycemia (PS4; PMID: 30259503, 29927023, 29510678, 29207974, 29056535, 27256595, 25953829, 25555642, 24918535, 20337973, 19309449, 11508276, internal lab contributors). This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and three-generation, dominant family history of diabetes or hyperglycemia in a family not used for PP1) (PP4_Moderate; internal lab contributors). This variant segregated with diabetes/hyperglycemia, with 13 informative meioses in one family with MODY (PP1_Strong; internal lab contributors). Another missense variant, c.571C>T p.(Arg191Trp), has been classified as pathogenic by the ClinGen MDEP but has a greater Grantham distance than p.(Arg191Gln) (PM5_Supporting). In summary, c.572G>A meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.3.0, approved 8/11/2023): PP3, PP2, PM2_Supporting, PS4, PP1_Strong, PP4_Moderate, PM5_Supporting.
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PS4
This variant was identified in 39 unrelated individuals with hyperglycemia (PS4; PMID: 30259503, 29927023, 29510678, 29207974, 29056535, 27256595, 25953829, 25555642, 24918535, 20337973, 19309449, 11508276, internal lab contributors).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.873, which is greater than the MDEP VCEP threshold of 0.70 (PP3).
PP2
GCK is defined by the ClinGen MDEP as a gene that has a low rate of benign missense variation and has pathogenic missense variants as a common mechanism of disease (PP2).
PP4_Moderate
This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and three-generation, dominant family history of diabetes or hyperglycemia in a family not used for PP1) (PP4_Moderate; internal lab contributors).
PM5_Supporting
Another missense variant, c.571C>T p.(Arg191Trp), has been classified as pathogenic by the ClinGen MDEP but has a greater Grantham distance than p.(Arg191Gln) (PM5_Supporting).
PP1_Strong
This variant segregated with diabetes/hyperglycemia, with 13 informative meioses in one family with MODY (PP1_Strong; internal lab contributors).
Not Met criteria codes
PM3
PM3 (in trans): Only one hmz case due to consanguinity ​
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